.TH g_rmsf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_rmsf - calculates atomic fluctuations

.B VERSION 4.5
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-q" " eiwit.pdb "
.BI "\-oq" " bfac.pdb "
.BI "\-ox" " xaver.pdb "
.BI "\-o" " rmsf.xvg "
.BI "\-od" " rmsdev.xvg "
.BI "\-oc" " correl.xvg "
.BI "\-dir" " rmsf.log "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]res" ""
.BI "\-[no]aniso" ""
.BI "\-[no]fit" ""
.SH DESCRIPTION
\&g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard 
\&deviation) of atomic positions 
\&after (optionally) fitting to a reference frame.


\&With option \fB \-oq\fR the RMSF values are converted to B\-factor
\&values, which are written to a pdb file with the coordinates, of the
\&structure file, or of a pdb file when \fB \-q\fR is specified.
\&Option \fB \-ox\fR writes the B\-factors to a file with the average
\&coordinates.


\&With the option \fB \-od\fR the root mean square deviation with
\&respect to the reference structure is calculated.


\&With the option \fB aniso\fR g_rmsf will compute anisotropic
\&temperature factors and then it will also output average coordinates
\&and a pdb file with ANISOU records (corresonding to the \fB \-oq\fR
\&or \fB \-ox\fR option). Please note that the U values
\&are orientation dependent, so before comparison with experimental data
\&you should verify that you fit to the experimental coordinates.


\&When a pdb input file is passed to the program and the \fB \-aniso\fR
\&flag is set
\&a correlation plot of the Uij will be created, if any anisotropic
\&temperature factors are present in the pdb file.


\&With option \fB \-dir\fR the average MSF (3x3) matrix is diagonalized.
\&This shows the directions in which the atoms fluctuate the most and
\&the least.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-q" " eiwit.pdb" 
.B Input, Opt.
 Protein data bank file 

.BI "\-oq" " bfac.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-ox" " xaver.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-o" " rmsf.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-od" " rmsdev.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oc" " correl.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-dir" " rmsf.log" 
.B Output, Opt.
 Log file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]res"  "no    "
 Calculate averages for each residue

.BI "\-[no]aniso"  "no    "
 Compute anisotropic termperature factors

.BI "\-[no]fit"  "yes   "
 Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
